I'm reposting this from askubuntu.com, as it was discussed fairly quickly that Ubuntu's presence on a separate partition was almost certainly NOT the problem, and as such this question wasn't appropriate there.
I recently restored a Toshiba laptop using its recovery partition, which claims to revert Windows 7 "back to factory settings". It booted up, shut down just fine. I opted to restore to ~100GB of the disk, leaving the other partition blank.
I then installed Ubuntu 12.04 on the other partition (slightly larger than the Win7 side, ~120GB), booted that side up, installed 360+ updates and found this partition to work correctly.
Did a startup-shutdown on both OSes, seemed to be okay.
I then used the Win 7 side for a bit, and it found its own updates to install. I left this to update itself (probably a mistake) and came back later to find that the updates were not finished, but also that the Windows 7 OS had encountered difficulty shutting down. I hard powered it off, as it had been left to its own device for quite some time (overnight, truthfully - I fell asleep, d'oh) and restarted. Seemed fine, the update process continued. I powered it down again. It hung again just after the "Shutting down" screen.
It appears to do everything correctly, right up until it would actually power down. Screen fades to black, but the fans never turn off.
The Ubuntu partition is fine, great actually. Seems unaffected by whatever may have happened.
What could have caused this, and what's more, can I fix this without doing another recovery? Since this computer was given to me, I do not have a recovery or boot disk for the Windows 7 partition, and it is my understanding that Windows recovery/boot disks do not play nicely with existing separate partitions.
I'm at work right now, but if it would help to post an lshw or a dxdiag please let me know and I can do this as I have access to the laptop later tonight.